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BioC 3.6: CHECK report for podkat on malbec1

This page was generated on 2017-08-16 13:23:05 -0400 (Wed, 16 Aug 2017).

Package 1012/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.9.0
Ulrich Bodenhofer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/podkat
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: podkat
Version: 1.9.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.9.0.tar.gz
StartedAt: 2017-08-16 01:27:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:31:50 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 285.1 seconds
RetCode: 0
Status:  OK 
CheckDir: podkat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/podkat.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘podkat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘podkat’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘podkat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
unmaskedRegions   21.604  0.968  27.577
plot-methods      10.040  0.428  10.477
assocTest-methods 10.176  0.264  10.445
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/podkat.Rcheck/00check.log’
for details.


podkat.Rcheck/00install.out:

* installing *source* package ‘podkat’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_podkat.cpp -o R_init_podkat.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bernoulliExact.cpp -o bernoulliExact.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cumMax.cpp -o cumMax.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c doubleMale.cpp -o doubleMale.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c kernels.cpp -o kernels.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pValues.cpp -o pValues.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c partitionRegions.cpp -o partitionRegions.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c qfc.cpp -o qfc.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/podkat.Rcheck/podkat/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘p.adjust’ from package ‘stats’ in package ‘podkat’
Creating a generic function for ‘qqplot’ from package ‘stats’ in package ‘podkat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (podkat)

podkat.Rcheck/podkat-Ex.timings:

nameusersystemelapsed
AssocTestResult-class1.1160.0281.146
AssocTestResultRanges-class1.7440.0041.749
GenotypeMatrix-class3.0840.0243.110
NullModel-class1.8560.0041.862
VariantInfo-class0.2160.0000.216
assocTest-methods10.176 0.26410.445
computeKernel0.0360.0000.035
filterResult-methods1.8160.0001.817
genotypeMatrix-methods0.8160.0040.822
hgA0.0160.0000.017
nullModel-methods0.7280.0120.740
p.adjust-methods1.060.001.06
partitionRegions-methods0.6520.0040.657
plot-methods10.040 0.42810.477
podkat-package1.1080.0001.111
print-methods1.1320.0001.133
qqplot-methods2.0920.0002.094
readGenotypeMatrix-methods0.1720.0040.177
readRegionsFromBedFile0.0440.0000.045
readSampleNamesFromVcfHeader0.0120.0000.013
readVariantInfo-methods0.2560.0000.258
sort-methods1.1320.0041.138
split-methods1.9800.0001.983
unmasked-datasets0.4760.0000.477
unmaskedRegions21.604 0.96827.577
weightFuncs0.0040.0000.005
weights-methods1.2280.0001.226